DNA sequence design by dynamic neighborhood searches

Suguru Kawashimo; Hirotaka Ono; Kunihiko Sadakane; Masafumi Yamashita

doi:10.1007/11925903_12

DNA sequence design by dynamic neighborhood searches

Suguru Kawashimo, Hirotaka Ono, Kunihiko Sadakane, Masafumi Yamashita

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

19 Citations (Scopus)

Abstract

We propose a local-search based algorithm to design DNA sequence sets that satisfy several combinatorial constraints about hamming-distance criteria. To deal with the constraints in the local search, we adopt elaborate (and dynamic) neighborhood search frameworks called the Variable Neighborhood Search (VNS) and the Variable Depth Search (VDS). Although our algorithm can deal with many types of hamming distance-based constraints and is easy to extend (e.g., also applicable for other constraints), in computational experiments, we succeeded in generating better sequence sets than the ones generated by exiting methods of more specified constraints.

Original language	English
Title of host publication	DNA Computing - 12th International Meeting on DNA Computing, DNA12, Revised Selected Papers
Pages	157-171
Number of pages	15
DOIs	https://doi.org/10.1007/11925903_12
Publication status	Published - 2006
Event	12th International Meeting on DNA Computing, DNA12 - Seoul, Korea, Republic of Duration: Jun 5 2006 → Jun 9 2006

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	4287 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Other

Other	12th International Meeting on DNA Computing, DNA12
Country/Territory	Korea, Republic of
City	Seoul
Period	6/5/06 → 6/9/06

All Science Journal Classification (ASJC) codes

Theoretical Computer Science
General Computer Science

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10.1007/11925903_12

Cite this

Kawashimo, S., Ono, H., Sadakane, K., & Yamashita, M. (2006). DNA sequence design by dynamic neighborhood searches. In DNA Computing - 12th International Meeting on DNA Computing, DNA12, Revised Selected Papers (pp. 157-171). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4287 LNCS). https://doi.org/10.1007/11925903_12

DNA sequence design by dynamic neighborhood searches. / Kawashimo, Suguru; Ono, Hirotaka; Sadakane, Kunihiko et al.
DNA Computing - 12th International Meeting on DNA Computing, DNA12, Revised Selected Papers. 2006. p. 157-171 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4287 LNCS).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Kawashimo, S, Ono, H, Sadakane, K & Yamashita, M 2006, DNA sequence design by dynamic neighborhood searches. in DNA Computing - 12th International Meeting on DNA Computing, DNA12, Revised Selected Papers. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 4287 LNCS, pp. 157-171, 12th International Meeting on DNA Computing, DNA12, Seoul, Korea, Republic of, 6/5/06. https://doi.org/10.1007/11925903_12

Kawashimo S, Ono H, Sadakane K, Yamashita M. DNA sequence design by dynamic neighborhood searches. In DNA Computing - 12th International Meeting on DNA Computing, DNA12, Revised Selected Papers. 2006. p. 157-171. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/11925903_12

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DNA sequence design by dynamic neighborhood searches

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